Umar Patek, 45, who faces the death penalty if convicted, made the apology in West Jakarta court, The Daily Telegraph of Britain reported.
"I am taking this opportunity to seek forgiveness from the victims, their families and whoever else suffered losses," Patek said.
"I am very sad and regret the incident, because I was against it from the start. I never agreed to their methods," he added, referring to the al-Qaida-linked group Jemaah Islamiyah.
Patek is charged with premeditated murder, bomb-making and illegal firearms possession.
He denied assembling bombs or loading them into a car.
Patek was arrested last year in Abbottabad, Pakistan, before the killing of Osama bin Laden by U.S. forces in the same town. Patek was later extradited to Indonesia.
Patek said he did not know nightclubs would be the targets but said he knew the bombings would target foreigners in revenge for killings of Muslims in the Palestinian territories.
"I questioned, 'Why Bali?'" Patek said. "Jihad should be carried out in Palestine instead. But they said they did not know how to get to Palestine."
Another bomber killed in a police raid told him "not to think so hard, just help," Patek said.